BIEN R package

Brian Maitner

2018-05-09

The Botanical Information and Ecology Network(BIEN) R package provides access to the BIEN database as well as useful tools for working with the BIEN data.

Data Usage Agreement

Please read the data usage agreement, available at: http://bien.nceas.ucsb.edu/bien/biendata/data-use-policy/

Data Usage: Warnings and Caveats

Please be aware of quality and appropriateness of BIEN data for the analyses that you may wish to perform or information that you would like to obtain

Versioning - data available via BIENdata.org and the the BIEN R package (BIEN) are being updated and improved. This is an active collaborative group who is aiming to continue to improve the quality of botanical information and data. As a result, users should take note of the verison number (using the function BIEN_metadata_database_version() ) and be sure to check back periodically for updates. Checking for new results to a query can be done using the function BIEN_metadata_match_data().

Data quality - All data are presented ‘as is’. Default BIEN downloads return all data associated with a given taxonomic name string. There may be additional issues associated with a given name string. Please be aware that data returned may also include data whose geographic coordinates and cultivated status are uncertain or unverifiable.

Hybrids - Hybrid species are assigned the specific epithet “x” by the TNRS. To view the full name information for these occurrences, set “all.taxonomy = TRUE”.

Database connection issues

Some institution and computer programs (e.g. some antivirus programs) block the SQL connections that this package relies on. While we are exploring ways around this issue, at present the simplest method is to use the package on a computer/network that doesn’t block SQL connections.

Function Names

Function names in the BIEN package follow a naming convention which was designed to make locating the desired function easier:

Function Directory

For full information on each function, see the associated help file.

BIEN_metadata functions

BIEN_list functions

BIEN_occurrence functions

BIEN_ranges functions

BIEN_trait functions

BIEN_plot functions

BIEN_stem functions

BIEN_taxonomy functions

BIEN_phylogeny functions